Human Papilloma Viruses (HPV) are DNA-based pathogens that infect the epithelial surface of the skin and mucous membranes in humans and other animal species. Oncogenic strains of HPV have been associated with several human cancers including those of the cervix and anus. More recently, it has also been linked to squamous cell carcinoma of the head and neck region, specifically of the oropharynx. HPV induced oropharyngeal carcinoma has an increasing incidence in white males in the United States and Europe, and represents about 40-80% of all oropharyngealcarcinomas in the USA. Two viral oncogenes, E6 and E7, are invariably expressed in HPV-positive cancer cells. Their gene products are known to inactivate two major tumor suppressors, p53 and RB. Overtime, these effects of E6/E7 lead to the oncogenesis of infected epithelial cells in multiple locations, such as the oropharynx. HPV E6 and E7 are necessary for the oncogenic transformation, and therefore are invariably expressed in HPV induced tumors, and serve as biological markers for these tumors. Likewise, E6 and E7 expression may also function as surrogate markers to aid in prognosis assessment and evaluation of cancer response to treatment.